Student or Learner
What does "MAKE ONESELF" mean?
Alice said to Tom "Make yourself at home"
It's a specific phrase which can't really be broken down into its constituent parts. You'll hear "Make yourself at home" and sometimes "Make yourself comfortable". As Bhaisahab said, it basically just means "Please feel free to behave like you do at home". It should be noted, however, that that invitation only stretches so far.
If you are in the habit of walking around your own home naked and singing opera, it would be unwise to behave this way at someone else's house even if they say "Make yourself at home".
It basically means "Don't feel as if you have to behave formally or very politely just because you are in my home". You can sit down on the sofa, kick your shoes off and generally be comfortable.